GABPB1

GA binding protein transcription factor subunit beta 1, the group of Ankyrin repeat domain containing

Basic information

Region (hg38): 15:50275388-50355408

Previous symbols: [ "GABPB2" ]

Links

ENSG00000104064 ∙ NCBI:2553 ∙ OMIM:600610 ∙ HGNC:4074 ∙ Uniprot:Q06547 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GABPB1 gene.

• Inborn genetic diseases (2 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GABPB1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	2	1	0

Variants in GABPB1

This is a list of pathogenic ClinVar variants found in the GABPB1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
15-50286107-G-C		not specified	Uncertain significance (May 18, 2022)
15-50300891-C-T		not specified	Uncertain significance (Apr 27, 2023)
15-50301220-C-A			Likely benign (Nov 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GABPB1	protein_coding	protein_coding	ENST00000220429	8	78217

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.911	0.0888	124199	4	969	125172	0.00389

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.93	90	209	0.430	0.0000101	2545
Missense in Polyphen		17	70.52	0.24107		898
Synonymous	1.38	57	71.9	0.793	0.00000342	809
Loss of Function	3.64	3	21.0	0.143	0.00000130	222

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00481	0.00481
Ashkenazi Jewish	0.0116	0.0116
East Asian	0.00	0.00
Finnish	0.000278	0.000278
European (Non-Finnish)	0.00423	0.00422
Middle Eastern	0.00	0.00
South Asian	0.00707	0.00706
Other	0.00475	0.00476

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor capable of interacting with purine rich repeats (GA repeats). Necessary for the expression of the Adenovirus E4 gene. {ECO:0000269|PubMed:10675337, ECO:0000269|PubMed:8816484}.
• Pathway: Myometrial Relaxation and Contraction Pathways;Hematopoietic Stem Cell Gene Regulation by GABP alpha-beta Complex;Mitochondrial Gene Expression;Transcriptional activation of mitochondrial biogenesis;Mitochondrial biogenesis;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.194

Intolerance Scores

• loftool: 0.507
• rvis_EVS: 0.35
• rvis_percentile_EVS: 73.97

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.775
• ghis: 0.543

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.955

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Gabpb1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;mitochondrion organization;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm;cytoplasmic ribonucleoprotein granule
• Molecular function: DNA-binding transcription factor activity;protein binding;transcription regulatory region DNA binding;protein heterodimerization activity